{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":161311006,"defaultBranch":"master","name":"PGx-pipeline","ownerLogin":"molgenis","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2018-12-11T09:39:25.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/1688158?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1566972386.0","currentOid":""},"activityList":{"items":[{"before":"6db77a57a17d5f898fbe35980a8d5824c42c053f","after":"499c61fe9f6175f28fbf7f4c2e336f1f47bf3021","ref":"refs/heads/master","pushedAt":"2024-05-13T06:15:11.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"dennishendriksen","name":"Dennis Hendriksen","path":"/dennishendriksen","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/2477186?s=80&v=4"},"commit":{"message":"Updated imputation and phasing. Included protocols for CNV calling (#4)\n\n* updated gtc to final report\r\n\r\n* Split parameter stuff\r\n\r\n* Fixed parameter stuff\r\n\r\n* Fixed parameter stuff\r\n\r\n* Fixed parameter stuff\r\n\r\n* executable\r\n\r\n* Fixed parameter stuff\r\n\r\n* Fixed parameter stuff\r\n\r\n* Fixed parameter stuff\r\n\r\n* Fixed parameter stuff\r\n\r\n* Fixed parameter stuff\r\n\r\n* Fixed parameter stuff\r\n\r\n* Fixed parameter stuff\r\n\r\n* Fixed parameter stuff\r\n\r\n* Fixed parameter stuff\r\n\r\n* Fixed parameter stuff\r\n\r\n* Fixed indentation gtc_final_report.py\r\n\r\n* encapsulated code2genotype[genotype] with str function\r\n\r\n* encapsulated Alleles with str function\r\n\r\n* Added merge_final_reports.sh for merging final reports. We will use this for the input of opticall, and to run CNV calling on\r\n\r\n* Optimized parameters_pgx_pipeline.csv\r\n\r\n* Optimized parameters_pgx_pipeline.csv\r\n\r\n* Commented some molgenis compute parts that we are not working with currently\r\n\r\n* Commented some molgenis compute parts that we are not working with currently\r\n\r\n* Added protocol for the selection of variants\r\n\r\n* Now denoting window size without kb (in variant count)\r\n\r\n* Added protocol for preparing raw intensities for cnv calling\r\n\r\n* Added extra filtering for corrective variants\r\n\r\n* Added extra filtering for corrective variants\r\n\r\n* Added extra filtering for corrective variants\r\n\r\n* Added extra filtering for corrective variants\r\n\r\n* Added extra filtering for corrective variants\r\n\r\n* Fixed stage_intensities.sh\r\n\r\n* Fixed stage_intensities.sh\r\n\r\n* Fixed stage_intensities.sh\r\n\r\n* Added cnv calling, merging step in corrective_variants.sh, updated stage_intensities.sh to work with cnv-caller update\r\n\r\n* Preparation for filtering pgx genes\r\n\r\n* Preparation for filtering pgx genes\r\n\r\n* Fixed parameters_pgx_pipeline.csv\r\n\r\n* Fixed filter_pgx_genes.sh\r\n\r\n* Fixed filter_pgx_genes.sh\r\n\r\n* Fixed plink version for extracting with bed file\r\n\r\n* Fixed plink version in filter_pgx_genes.sh\r\n\r\n* Added protocol for merging PGx filtered plink datasets (merging chromosomes)\r\n\r\n* Fixed mistake\r\n\r\n* Updated protocols for pgx genes and imputation pipeline to facilitate a window region in phasing and imputation\r\n\r\n* Updated protocols for pgx genes and imputation pipeline to facilitate a window region in phasing and imputation\r\n\r\n* Updated main in imputation pipeline\r\n\r\n* Updated main in imputation pipeline\r\n\r\n* removed submodule\r\n\r\n* Updated readme of imputation pipeline\r\n\r\n* Updated nextflow java version\r\n\r\n* Updated pgx pipeline\r\n\r\n* Fixed imputation_pipeline.sh\r\n\r\n* fixed imputation nextflow pipeline for singularity on gs cluster\r\n\r\n* Fixing splitting into pgx genes\r\n\r\n* fixed problems\r\n\r\n* Now doing phasing on entire chromosome\r\n\r\n* Now doing phasing on entire chromosome\r\n\r\n* Renamed important variables\r\n\r\n* Renamed important variables\r\n\r\n* Renamed important variables\r\n\r\n* imputation pipeline\r\n\r\n* Updated slurm resources\r\n\r\n* Made sure that there is no attempt made to work with irrelevant chromsomes\r\n\r\n* Removed depricated pgx bed file references\r\n\r\n* Fixed mistake in input channel\r\n\r\n* Imputed imputation protocol and phasing time request\r\n\r\n* Fixed stuff\r\n\r\n* Base configuration\r\n\r\n* Updated cnv_calling script\r\n\r\n* Updated cnv_calling script\r\n\r\n* Correct path to cnv calling script\r\n\r\n* Now creating cyp2d6 bed file in protocol\r\n\r\n* Now creating cyp2d6 bed file in protocol\r\n\r\n* Corrected protocol for cnv calling\r\n\r\n* Corrected protocol for cnv calling\r\n\r\n* Corrected protocol for cnv calling\r\n\r\n* cnv calling update\r\n\r\n* Corrected variant files\r\n\r\n* Corrected protocol for staging intensities\r\n\r\n* Corrected protocol for preparing variant lists\r\n\r\n* changed protocol for preparing intensities\r\n\r\n* stage intensites\r\n\r\n* Added setting TMPDIR to prevent awk to exit\r\n\r\n* Added quotes around bash variables to prevent chellcheck to report issues\r\n\r\n* Added quotes around bash variables to prevent chellcheck to report issues\r\n\r\n* updated protocols\r\n\r\n* Also writing samplesheet samples that map to the sample mapping file\r\n\r\n* Filtering samples that pass QC\r\n\r\n* Added protocol for listing Qc'ed samples\r\n\r\n* Added protocol for listing Qc'ed samples\r\n\r\n* Renamed script map_genotype_samples.R\r\n\r\n* Renamed script map_genotype_samples.R\r\n\r\n* Corrected corrective_variants.sh to match argument parser of cnv caller\r\n\r\n* Corrected typo\r\n\r\n* Split cnv calling protocol in a calling and fit+ transform protocol. The latter of which represents the previous version\r\n\r\n* Split cnv calling protocol in a calling and fit+ transform protocol. The latter of which represents the previous version\r\n\r\n* Split cnv calling protocol in a calling and fit+ transform protocol. The latter of which represents the previous version\r\n\r\n* Now making directory for cnv output\r\n\r\n* Updated opticall protocols to work without molgenis\r\n\r\n* Added code for debugging\r\n\r\n* Added code for debugging\r\n\r\n* Trying to make it work\r\n\r\n* Trying to make it work\r\n\r\n* Trying to make it work without molgenis\r\n\r\n* trying to make it work without molgenis\r\n\r\n* corrected opticall protocol\r\n\r\n* Added protocols and scripts for autosomal quality control\r\n\r\n* forwarding parameters is now optional. Writing all parameters to params is preferred\r\n\r\n* Fixed mistake with making directory\r\n\r\n* Fixed mistake with making directory\r\n\r\n* implemented test for checking if sex-chromosome files are still in the general qc dir.\r\n\r\n* updated pipeline scripts and parameters\r\n\r\n* Keeping variants not shared by GH reference\r\n\r\n* Proper ordering of vcf\r\n\r\n* updated imputation main\r\n\r\n* Added sort after fixref\r\n\r\n* Removed GH from imputation pipeline\r\n\r\n* Removed GH from imputation pipeline\r\n\r\n* Removed GH from imputation pipeline\r\n\r\n* Removed GH from imputation pipeline\r\n\r\n* Updated imputation pipeline to remap a number of predefined indels\r\n\r\n* resolved imputation pipeline\r\n\r\n* Added make bed to fix indels\r\n\r\n* Removed filtering of monomorphic snps\r\n\r\n* Removed filtering of monomorphic snps\r\n\r\n* Exporting to vcf version 4.2 since vcftools is not able to handle 4.3\r\n\r\n* updated parameters\r\n\r\n* added indexing to imputation pipeline\r\n\r\n* Added scripts for normalizing indels in pharmvar tables\r\n\r\n* Resolved issue\r\n\r\n* Resolved issue\r\n\r\n* Also updating start and stop now\r\n\r\n* updated normalization\r\n\r\n* Also updating start and stop now\r\n\r\n* Also updating start and stop now\r\n\r\n* added annotation step in imputation pipeline\r\n\r\n* Updated imputation pipeline run script\r\n\r\n* Updated imputation pipeline run script\r\n\r\n* Fixed error\r\n\r\n* Fixed error\r\n\r\n* Fixed error\r\n\r\n* Fixed error\r\n\r\n* Fixed error\r\n\r\n* Adding vcf annotations\r\n\r\n* Added a script for fixing indels in a comprehensive fashion\r\n\r\n* Added a script for fixing indels in a comprehensive fashion\r\n\r\n* Added a script for fixing indels in a comprehensive fashion\r\n\r\n* Added a script for fixing indels in a comprehensive fashion\r\n\r\n* Added samtools to package\r\n\r\n* Update to container image\r\n\r\n* Update to container image\r\n\r\n* Updated resources for fix indels\r\n\r\n* fixes\r\n\r\n* Updated resources for fix indels\r\n\r\n* Added correct publishder\r\n\r\n* Added correct publishder\r\n\r\n* Added correct publishder\r\n\r\n* Added protocols for variant filtering and integrating genotype calls from cyp2d6 cnv calling\r\n\r\n* fixes\r\n\r\n* Added workflow scripts and parameter template file\r\n\r\n* Added workflow for converting gtc files to final report files\r\n\r\n* added parameter template file. adapted protocol for variant filtering\r\n\r\n* fixed\r\n\r\n* fixed errors in variant filtering\r\n\r\n* disregarding chr X for now\r\n\r\n* now starting stage intensities met txt.gz files\r\n\r\n* config\r\n\r\n* Modified pipeline to prepare annotated vcf for asterix, and prune to only those samples that need to get a passport\r\n\r\n* Modified pipeline to prepare annotated vcf for asterix, and prune to only those samples that need to get a passport\r\n\r\n* fixes","shortMessageHtmlLink":"Updated imputation and phasing. Included protocols for CNV calling (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"1171105475\" data-permission-text=\"Title is private\" data-url=\"https://github.com/molgenis/PGx-pipeline/issues/4\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/molgenis/PGx-pipeline/pull/4/hovercard\" href=\"https://github.com/molgenis/PGx-pipeline/pull/4\">#4</a>)"}}],"hasNextPage":false,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAESA7PiwA","startCursor":null,"endCursor":null}},"title":"Activity · molgenis/PGx-pipeline"}